What'sNEW April - June 2015

30 Jun 2015
MIT's CodePhage Fixes Software Bugs With Biologically Inspired Gene Swapping by Giulio Prisco, Hacked, 30 Jun 2015. Thanks Thanks, Google Alerts.
> Can Computers Mimic Darwinian Evolution? mentions possibly useful computer viruses.

24 Jun 2015
Today is Fred Hoyle's 100th birthday. Thanks Thanks,
George Nickas.
A Man Who Changed the Way We See the World (local docx), by Kamala Wickramasinghe, 2015.

The Origin of Life Circus
23 Jun 2015
The Origin of Life Circus, by Suzan Mazur fascinated us. She has interviewed about 40 of the major participants in origin-of-life research, and now she has published the entire collection. For the latest, frankest conversations in this field, you can't do better. She is well-informed on the science (and politics) of the subject, and the interviewees respond to her knowledge. Their research approaches may be top-down or bottom-up, in categories from metabolists, to compartmentalists, to geneticists. Interesting things are going on at the chemistry fringes, and bold predictions for synthetic life, relevancy unclear, are in the air. Outright pessimism is, of course, taboo.

We think origin-of-life research will be as fruitful as medieval alchemy: some things will be learned but the goal will prove impossible. We found no reason to reconsider. The whole field seems to be fragmented and in full retreat. The researchers are looking for easier questions, unconceived breakthroughs, or new, unimagined approaches. And the software problem is barely mentioned. Computers are being reassigned to the hardware problem! Huh?

Suzan Mazur spent over two years researching the origin of life investigation. She has been a journalist for four decades, reporting on a range of topics including evolution, scientific hoaxes and regional wars; and frequently published in The Economist, Financial Times and Huffington Post. Her previous book, Altenberg 16: An Exposé of the Evolution Industry, was published in 2010.

The real problem is to make ordered sequences of amino acids, and of course ordered sequences of nucleic acids -- and on that the prebiotic RNA world is absolutely silent. — Pier Luigi Luisi, p 397
< 25 Apr 2020: The Emergence of Life, by Luisi
Suzan Mazur, The Origin of Life Circus, 492 pages/US$28, ISBN:978-0-692-30849-3, publicised, 3 Jan 2015.
Book review by Adrian Bejan, NASA Astrobiology Focus Group, 5 Mar 2015.
> The RNA World And Other Origin-of-Life Theories is the main related CA webpage.

22 Jun 2015 What'sNEW about HGT |
Luis P. Villarreal How can evolutionary science not be talking about viruses when genomes are so heavily colonized by these entities?
Luis P. Villarreal, interviewed by Suzan Mazur, Huffington Post, online 17 Mar (accessed 22 Jun) 2015.
>2000 >2006 >2006 >2014: more from Villarreal.
Viruses are the unending front of evolution...they continue to shape the trajectory of life on the planet, including that of humans.
Luis Villarreal: A Life in Viruses, 13 May 2016.
> Viruses and Other Gene Transfer Mechanisms is a related webpage.

17 Jun 2015
Several Mars meteorites contain methane, according to a team including geochemists from Canada and the UK. The publicity is cautious, mentioning that some methane on earth comes from volcanoes. (But we wonder, could even that methane have been first made by methanogens?) Anyway, the abstract concludes, The occurrence of methane in Martian rock samples adds strong weight to models whereby any life on Mars is/was likely to be resident in a subsurface habitat, where methane could be a source of energy and carbon for microbial activity. So, regardless of the source, methane on Mars could at least nourish life there.
Nigel J. F. Blamey et al., "Evidence for methane in Martian meteorites" [
abstract], doi:10.1038/ncomms8399, n 7399 v 6, Nature Communications, 16 Jun 2015.
Methane in Mars Meteorites Suggests Possibility of Life by Charles Q. Choi, Space.com, 16 Jun 2015.
Scientists Find Methane in Mars Meteorites, Newswise, 17 Jun 2015. Thanks Thanks, Doron Goldberg.
> Life on Mars! is a related CA webpage (search for "methane"). Also see:
3 Jun 2015: Research suggests that methanogens could survive on Mars.

Astrobiology cover
17 Jun 2015
I am very puzzled as to why this major scientific question has been allowed to sit idle, unattended, for four decades — Gil Levin

Nearly Forty Years after Viking: Are We Ready for a New Life-Detection Mission? a panel discussion among John D. Rummel, Steven A. Benner, Gilbert Levin, Victor Parro, and Samuel Kounaves; moderated by Dirk Schulze-Makuch; doi:10.1089/ast.2015.1336, p 413-419 v 15, Astrobiology, 10 Jun 2015.
Thanks Thanks, William Smith.
> Life on Mars! and > Bacteria... are related CA webpages.

14-19 Jun 2015
Eric Hand, Daniel Clery, "The return of Philae" [
summary], Science, 19 Jun 2015.
Revived Philae poised to do comet science by Elizabeth Gibney, Nature News, 16 Jun 2015.
Rosetta's lander Philae wakes up from hibernation, ESA (+Rosetta Blog), 14 Jun 2015.
Philae comet lander wakes up, says ESA, BBC News, 14 Jun 2015. Thanks Thanks, NPR.
> What'sNEW under Comet Rendezvous has links to Rosetta updates.

SPIE logo
6 Jun 2015
Astrobiology returns to San Diego as part of the annual SPIE Conference, August 2015. Richard Hoover, Chandra Wickramasinghe and Gil Levin will chair the three-day program with 40 presentations including a Centenary Tribute to Sir Fred Hoyle.
Instruments, Methods, and Missions for Astrobiology XVII, San Diego, 9-11 Aug 2015.

3 Jun 2015
Research suggests that methanogens could survive on Mars. The study was presented at the 2015 General Meeting of the American Society for Microbiology, in New Orleans, 30 May - 2 Jun. Maybe the methane plumes on Mars come from life!
Earth Organisms Survive Under Low-Pressure Martian Conditions, University of Arkansas (+Newswise), 1 Jun 2015.
> Life on Mars! is a related CA webpage (search for "methane").

1 Jun 2015
Princeton Class of 1970 logo Science Under Attack! That was the title of an hour-long forum at Princeton University on Saturday afternoon, 29 May. Among the five Princeton panelists were Seth Shostak, '65, Senior Astronomer at the Center for SETI Research, and Peter Brown, '70, former editor of The Sciences and Natural History magazines. During open discussion I attempted to suggest that most evidence and arguments against the standard theory of evolution, including some I mentioned, are not attacks on Science, and it is rigid, blind and self-defeating for scientists to automatically react that way. The moderator interrupted me, clearly dreading another attack on science. Shostak politely responded that science depends on evidence, theories can only be replaced by better theories, and theories need to make predictions. For a prediction, I offered Horizontal Gene Transfer. Brown acknowledged that 40% of bacterial genes were acquired by transfer. Actually it may be as much as 100%, whereas 0% was the prediction of standard darwinism. I was grateful for cordiality from Shostak and Brown, but the message flopped. Panspermia was never mentioned, and science survived.
> Evolution vs Creationism is a related CA webpage.

Presenting science as a battle for truth against ignorance is an unhelpful exaggeration.
Beware the anti-science label, Nature, 10 May 2017.
The question is entirely scientific; ignoring it is not.
Skepticism About Evolution by Brig Klyce, Princeton Alumni Weekly, online 06 Jul 2017.

31 May 2015
For all the satellites and rovers that have studied Mars since [Viking], there has been no sign of so much as a bacterium. Right, because we sent no more instruments capable of detecting any. Besides, methane is a sign of methanogens. But at least Liquid water ...may still sometimes be seen at the surface. That admission took a long time.

What about life on icy moons? —
If a probe flying through a watery plume picked up a cargo of left-handed amino acids, that would pretty much close the case on whether there are aliens on Enceladus. Now NASA is considering a mission to Enceladus, perhaps jointly with JAXA, Japan's space agency. (But why don't left-handed amino acids also close the case for past life on the parent bodies of meteorites like Murchison?)

"Waterworlds," p 78-79, The Economist, 30 May 2015.
> Life on Mars! and > Life on Europa...? are related CA webpages.

Comet 67P from 19.9 km
Comet 67P as seen from ESA's Rosetta spacecraft at a distance 19.9 km, on 28 Mar 2015. About 3.1 x 1.7 km of the big lobe of the comet is pictured.
CometWatch 28 March - 14 km flyby, Rosetta Blog, ESA, posted 1 Apr 2015.
> What'sNEW under Comet Rendezvous has links to Rosetta updates.

17 May 2015
Europa The discolored cracks of the Jovian moon Europa could suggest life.
Life in Space? The Odds Just Went Up by Jeffrey Kluger, Time, 13 May 2015.
...Europa's Mystery Dark Material Could Be Sea Salt, NASA JPL, 12 May 2015.
K.P. Hand and R.W. Carlson, "Europa's surface color suggests an ocean rich with sodium chloride" [abstract], doi:10.1002/2015GL063559, Geophysical Research Letters, online 15 May 2015.
> Life on Europa, Other Moons, Other Planets?... is a related CA webpage. Thanks Thanks, William Smith.

7 May 2015 What'sNEW about HGT |
So indeed, the new understanding of evolution needs to integrate what we now know about viruses and virus-host interactions which, from my own perspective, has been absolutely one of the key factors of all evolution since the emergence of cells -- well, actually even before the emergence of cells.
...Eugene Koonin, interviewed by Suzan Mazur, Huffington Post, 7 May 2015.
Eugene V. Koonin's book, reviewed in What'sNEW, 20 Dec 2013.
> Viruses and Other Gene Transfer Mechanisms is a related webpage.

7 May 2015
...An Interview with Ford Doolittle by Jane Gitschier, PLoS Genet, 7 May 2015.
> Introns..., > Why Sexual Reproduction? and > The Tree of Life are related local webpages.

7 May 2015 What'sNEW about HGT |
Numerous genes for Eukaryotic Signature Proteins (ESPs) have been found in Archaea. The newly observed ESP homologues include genes for actin, tubulin and several information-processing proteins involved in transcription and translation. The highest number of them, 175, were observed in Lokiarchaeum, a lineage of archaea found in mud deep under the ocean. (ESPs are denoted "Eukarya" in the bar-graphs.) The European researchers speculate that eukaryotes descended via an ancestor shared with this lineage. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes. ...Taken together, our data indicate that the archaeal ancestor of eukaryotes was even more complex than previously inferred....

Phylogenetic breakdown of 4 archaeal proteomes By darwinian logic, they must suppose that the ESPs are not, after all, eukaryote-specific. Otherwise, why are the genes already there? Although the function of these hypothetical gelsolin-domain proteins remains to be elucidated, it is tempting to speculate that Lokiarchaeum has a dynamic actin cytoskeleton. ...These findings suggest an archaeal ancestor of eukaryotes that might have been more complex than the archaeal lineages identified thus far. Yet, the absence of missing links in the prokaryote-to-eukaryote transition currently precludes detailed predictions about the nature and timing of events that have driven the process of eukaryogenesis....

In cosmic ancestry, "new" genes aren't really new. Instead, they must exist before they can be deployed. (We would be required to rethink if genes were never seen to precede the features they encode.) And we notice that unfamiliar genes (black in bar-graphs) continue to appear in high proportion to all genes, a complete surprise for darwinism. (As more genomes are sequenced, the missing relatives should be found.)

Anja Spang, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka et al., "Complex archaea that bridge the gap between prokaryotes and eukaryotes" [
abstract], doi:10.1038/nature14447, p 173-179; ...and commentary: T. Martin Embley and Tom A. Williams, "Evolution: Steps on the road to eukaryotes" [abstract], doi:10.1038/nature14522, p 169-170 ...v 521 Nature, 14 May (online 6 May) 2015.
Mitch Leslie, "Deep-ocean microbe is closest living relative of complex cells" [summary], doi:10.1126/science.348.6235.615, Science, 8 May 2015.
Missing Link Microbes May Help Explain How Single Cells Became Us by Nell Greenfieldboyce, NPR, 6 May 2015.
Researchers discover missing link in the evolution of complex cells, Uppsala University (+PhysOrg.com), 7 May 2015.
Newly found microbe is close relative of complex life by Paul Rincon, BBC News, 6 May 2015.
Prokaryotic Microbes with Eukaryote-like Genes Found by Jyoti Madhusoodanan, The Scientist, 6 May 2015.
Thanks Thanks, Stan Franklin and Bob Sweeney.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.
> Metazoan Genes Older Than Metazoa? and > Genes Older Than Earth? are related local webpages.
9 Oct 2015: ...Comparative analysis of eukaryotic cells and genomes indicates that the signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor....
The trickster microbes that are shaking up the tree of life, doi:10.1038/d41586-019-01496-w, Nature, 14 May 2019.

28 Apr 2015 What'sNEW about HGT |
Retroelement-containing ANMV-1 genome Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. This introductory comment comes from a study that found, for the first time, DGRs in archaea. (They were observed in bacteria and their viruses at least a decade ago.) In one example from the new study, a virus targets the nucleotides encoding specific protein domains, with the potential to generate more than 10^18 protein variants (equivalent to 14 unrestricted amino acids.) Also, DGRs were noticed in the sequenced genomes of two nanoarchaea, where they appear to target orphan genes.

Crucially, the reverse transcriptase (RT) used is error-prone at template adenine bases, but has high fidelity at other template bases.... We suspect that analogous mechanisms may be available throughout life. How this would happen among eukaryotes is not well-understood, but for prokaryotes, the mechanisms are now becoming apparent. Directed mutation would be an important part of the genetic software management systems required in cosmic ancestry. ...Massive and low-risk protein diversification offers clear advantages to any organism....

Blair G. Paul et al., "Targeted diversity generation by intraterrestrial archaea and archaeal viruses" [full], doi:10.1038/ncomms7585, n 6585 v 6, Nature Communications, 23 Mar 2015.
> 09 Oct 2004: an example of a viral gene that generates diversity in bacteria.
> How is it Possible? mentions directed mutation. > Introns... mentions retrohoming.
> Neo-Darwinism discusses the mainstream theory of evolution.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.
> Robust Software Management in Genomes is a new related, incomplete webpage.

22 Apr 2015 What'sNEW about HGT |
HERVK expression We may owe our survival and complexity to a stowaway virus that springs to life in the very first cells of human embryos. Not only does the virus seem to protect embryos from other viruses, but it also assists genes when the groundwork is under way for the body plan of a new human. So says New Scientist, after a research team from Stanford and affiliated institutions uncovered surprising, important roles for endogenous retroviruses (ERVs), starting at the eight-cell stage of human embryogenesis.

Edward J. Grow et al., "Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells" [abstract], doi:10.1038/nature14308, Nature, online 20 Apr 2015.
Virus hiding in our genome protects early human embryos by Andy Coghlan, New Scientist, 20 Apr 2015.
> Viruses and Other Gene Transfer Mechanisms is a related CA webpage.
Thanks Thanks, Kevin Hatfield.

Nathalie Cabrol
20 Apr 2015
The hypothesis that there is still life present on Mars today remains a viable one — Nathalie Cabrol, SETI Institute. In addition to Mars, she discusses high deserts on Earth analogous to early Mars, and what we can learn from them.

How Mars might hold the secret to the origin of life, TED talk by Nathalie Cabrol, 18 March 2015.
Nathalie Cabrol Looks for Life on Mars by Alexandra Wolfe, The Wall Street Journal, 17 Apr 2015.
Earth and Mars May Have Shared Seeds of Life by Nola Taylor Redd, Astrobiology Magazine posted on Space.com, 25 Jun 2015.
Thanks Thanks for alerts, Jim Buchman and Ronnie McGhee.
> Life on Mars! and > Life on Europa, Other Moons, Other Planets?... are related.

18 Apr 2015
galaxy at redshift of z = ~7.5 A galaxy less than 2% as old as the universe had already formed much of its stars and metals, according to European astrophysicists and cosmologists. The galaxy has a redshift of z = ~7.5, which corresponds to a distance of c. 13.6 billion lightyears. The investigators were able to see a galaxy so remote only because its image was magnified 9.3x by gravitational lensing, produced by fortuitous alignment with an intervening galactic cluster. (The zoomed box in the illustration is 4" x 4".) The supposed lack of metals in the very early universe would theoretically preclude the existence of life then. But the metals appear to be there.

Darach Watson et al., "A dusty, normal galaxy in the epoch of reionization," doi:10.1038/nature14164, p 327-330 v 519, Nature, 19 Mar 2015.
Hubble law and the expanding universe - HyperPhysics, from Georgia State University, has an algorithm for Hubble Distance Calculation. For z=7.5, distance=13596.76 Mly (million lightyears).
> The End and the Big Bang is a related local webpage.
> Very young galaxies contain the heavy elements needed for life, What'sNEW, 5 Jun 2012.
> Galaxies theoretically young look old, What'sNEW, 9 Jun 2006.

14 Apr 2015
Philae came to rest almost two hours after touchdown on comet 67P/Churyumov-Gerasimenko, 12 Nov 2014. Rosetta's comet-lander initially bounced 123 meters high and flew 631 meters before coming back down. Then it bounced even higher and traversed another 641 meters. With a final small bounce, it settled onto the surface. The reconstruction of this trajectory comes from ESA's team who gathered data to analyze the magnetic field of the comet.
Hans-Ulrich Auster et al., "The nonmagnetic nucleus of comet 67P/Churyumov-Gerasimenko" [
abstract], doi:10.1126/science.aaa5102, Science, online 14 Apr 2015.
> What'sNEW under Comet Rendezvous has links to earlier Rosetta updates.
> Comets... is a related local webage.

Philae's landing path
The mosaic from OSIRIS images displays the horizontal path of Philae (top) on the surface of 67P/Churyumov-Gerasimenko. The ballistic trajectory (dark blue) and the surface profile (black) indicate the flight of Philae above the surface.... [adapted from Auster et al., 2015]

7 Apr 2015
Ellen Stofan, NASA chief scientist I think we're going to have strong indications of life beyond Earth within a decade, and I think we're going to have definitive evidence within 20 to 30 years. Ellen Stofan (pictured), NASA chief scientist, makes these comments during an hour-long panel discussion, "Solar System and Beyond: The Search for Water and Habitable Planets," in Washington DC today. Also, John Grunsfeld, former astronaut and NASA Associate Administrator said, Mars ...is currently a habitable environment.

Water in the Universe: YouTube video of the NASA panel discussion, 7 Apr 2015.
NASA Chief Scientist Predicts Signs Of Alien Life Within 10 Years by Ed Mazza, Huffington Post, 8 Aug 2015.
Thanks Thanks David Darling via facebook, and George Stratton.
> Life on Mars! and > Life on Europa, Other Moons, Other Planets?... are among related CA webpages.

Astrobiology, the study of the origin, evolution, distribution, and future of life in the universe, will be explored at a conference in Kandy, Sri Lanka, 21-23 August 2015. Chandra Wickramasinghe is the conference chairman and The University of Peradeniya is the host.
Astrobiology Research Conference 2015: PDF with information, registration, conference dates: 21-23 Aug 2015.
International Research Center, University of Peradeniya.
International Research Center, University of Peradeniya
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